Product-specific reaction kinetics in continuous uniform supersonic flows probed by chirped-pulse microwave spectroscopy.

Experimental studies of the products of elementary gas-phase chemical reactions occurring at low temperatures (<50 K) are very scarce, but of importance for fundamental studies of reaction dynamics, comparisons with high-level quantum dynamical calculations, and, in particular, for providing data for the modeling of cold astrophysical environments, such as dense interstellar clouds, the atmospheres of the outer planets, and cometary comae. This study describes the construction and testing of a new apparatus designed to measure product branching fractions of elementary bimolecular gas-phase reactions at low temperatures. It combines chirped-pulse Fourier transform millimeter wave spectroscopy with continuous uniform supersonic flows and high repetition rate laser photolysis. After a comprehensive description of the apparatus, the experimental procedures and data processing protocols used for signal recovery, the capabilities of the instrument are explored by the study of the photodissociation of acrylonitrile and the detection of two of its photoproducts, HC3N and HCN. A description is then given of a study of the reactions of the CN radical with C2H2 at 30 K, detecting the HC3N product, and with C2H6 at 10 K, detecting the HCN product. A calibration of these two products is finally attempted using the photodissociation of acrylonitrile as a reference process. The limitations and possible improvements in the instrument are discussed in conclusion.

Ulvans are not equal - Linkage and substitution patterns in ulvan polysaccharides differ with Ulva morphology.

Ulva are hardy green seaweeds that contain the sulfated polysaccharide ulvan and grow in two distinct morphologies: foliose and tubular. The authors hypothesise that ulvan from tubular species are more structurally complex than ulvans from foliose species. Herein, using standardised methods, the glycosyl linkage positions and sulfate ester substitutions of constituent monosaccharides of ulvan isolated from foliose (U. lacinulata and U. stenophylloides) and tubular (U. prolifera and U. ralfsii) species of Ulva were investigated. Comparison of native ulvans with 80 and 100 °C desulfated counterparts indicated that 4-linked rhamnose is predominantly 3-O-sulfated in all four ulvans. Ulvans from the foliose species predominantly contained →3,4)-Rhap-(1→, →4)-GlcAp-(1→ and →4)-IdoAp-(1→, collectively accounting for 67 to 81 mol% of the total linkages. In contrast, these same linkages in ulvans from the tubular species only collectively accounted for 29 to 36 mol%. Instead, ulvan from tubular species contained a combination of →2,3,4)-Rhap-(1→, terminal Rhap-(1→, →4)-GlcAp-(1→, →4)-Xylp-(1→, and/or →4)-Galp-(1→ in high proportions; some of the latter three residues were also likely O-2 sulfated. The results presented here suggest that ulvan from foliose species are predominantly unbranched polysaccharides composed of repeat disaccharides while ulvans from tubular species contain a greater diversity of branch and sulfate substitution locations.

The genome sequence of the Chequered Fruit-tree Tortrix, Pandemis corylana (Fabricius, 1794).

We present a genome assembly from an individual male Pandemis corylana (the Chequered Fruit-tree Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 441.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.53 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,608 protein coding genes.

Does harvesting age matter? Changes in structure and rheology of a shear-thickening polysaccharide from Cyathea medullaris as a function of age.

A shear-thickening polysaccharide from the New Zealand Black tree fern (Cyathea medullaris, commonly known as mamaku) extracted from different age fronds (stage 1: young, stage 2: fully grown and stage 3: old) was characterised in terms of structure and rheological properties. Constituent sugar analysis and 1H and 13C NMR revealed a repeating backbone of -4)-ß-D-GlcpA-(1 â†’ 2)-α-D-Manp-(1→, for all mamaku polysaccharide (MP) samples from different age fronds without any alterations in molecular structure. However, the molecular weight (Mw) was reduced with increasing age, from ~4.1 × 106 to ~2.1 × 106 Da from stage 1 to stage 3, respectively. This decrease in Mw (and size) consequently reduced the shear viscosity (ηs-Stage 1 > Î·s-Stage 2 > Î·s-Stage 3). However, the extent of shear-thickening and uniaxial extensional viscosity of MP stage 2 was greater than MP stage 1, which was attributed to a greater intermolecular interaction occurring in the former. Shear-thickening behaviour was not observed in MP stage 3.

The genome sequence of the Black-tipped Ermine, Yponomeuta plumbella (Denis & Schiffermüller, 1775).

We present a genome assembly from an individual male Yponomeuta plumbella (the Black-tipped Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence is 636.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length.

The genome sequence of the Round-winged Muslin, Thumatha senex (Hübner, 1804).

We present a genome assembly from an individual female Thumatha senex (the Round-winged Muslin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 810.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.

Novel 4-O-ß-d-xylopyranosyl-3,6-anhydro-l-galactopyranosyl disaccharide units in a polysaccharide from the red alga Pyrophyllon subtumens.

Thalli of the endemic epiphytic New Zealand red seaweed Pyrophyllon subtumens are known to contain a high level of xylose and a notable amount of arabinose but the extracted polysaccharide has not been characterised. The linkage/substitution of individual sugars within the water-soluble polysaccharide extract and various derivatives were determined by chemical and spectroscopic methods. No 3-linked sugars nor any d-galactose were found, which excluded agar-, carrageenan- or mixed 3-linked/4-linked ß-d-xylan-type polysaccharides found in many other red macroalgae. Instead, the polysaccharide backbone contained predominantly 4-linked ß-d-xylopyranosyl, 4-linked 3,6-anhydro-l-galactopyranosyl and 4-linked l-galactopyranosyl units. Some of each type of sugar were sulfated at various positions. Some xylosyl units were substituted at the 2- or 3-position with l-arabinosyl units. The polysaccharide is complex and likely contains a range of structures. However, partial sequencing was successfully used to recover and identify a novel disaccharide 4-O-d-xylopyranosyl-3,6-anhdydro-l-galactopyranose, which indicates a unique →4)-ß-d-Xylp-(1 â†’ 4)-3,6-anhydro-l-Galp-(1 â†’ repeat unit in the polysaccharide.

Collisional excitation of HNC by He found to be stronger than for structural isomer HCN in experiments at the low temperatures of interstellar space.

HCN and its unstable isomer HNC are widely observed throughout the interstellar medium, with the HNC/HCN abundance ratio correlating strongly with temperature. In very cold environments HNC can even appear more abundant than HCN. Here we use a chirped pulse Fourier transform spectrometer to measure the pressure broadening of HCN and HNC, simultaneously formed in situ by laser photolysis and cooled to low temperatures in uniform supersonic flows of helium. Despite the apparent similarity of these systems, we find the HNC-He cross section to be more than twice as big as the HCN-He cross section at 10 K, confirming earlier quantum calculations. Our experimental results are supported by high-level scattering calculations and are also expected to apply with para-H2, demonstrating that HCN and HNC have different collisional excitation properties that strongly influence the derived interstellar abundances.

Variability in the composition of porcine mucosal heparan sulfates.

Commercial porcine intestinal mucosal heparan sulfate (HS) is a valuable material for research into its biological functions. As it is usually produced as a side-stream of pharmaceutical heparin manufacture, its chemical composition may vary from batch to batch. We analysed the composition and structure of nine batches of HS from the same manufacturer. Statistical analysis of the disaccharide compositions placed these batches in three categories: group A had high GlcNAc and GlcNS, and low GlcN typical of HS; group B had high GlcN and GlcNS, and low GlcNAc; group C had high di- and trisulfated, and low unsulfated and monosulfated disaccharide repeats. These batches could be placed in the same categories based on their 1H NMR spectra and molecular weights. Anticoagulant and growth factor binding activities of these HS batches did not fit within these same groups but were related to the proportions of more highly sulfated disaccharide repeats.

The genome sequence of the Kent black arches, Meganola albula (Denis & Schiffermüller, 1775).

We present a genome assembly from an individual male Meganola albula (the Kent black arches; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 405 megabases in span. Most of the assembly (99.95%) is scaffolded into 30 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.

Structural characterization of ulvans extracted from blade (Ulva ohnoi) and filamentous (Ulva tepida and Ulva prolifera) species of cultivated Ulva.

Ulvans from Ulva ohnoi, Ulva tepida and Ulva prolifera were extracted under mild acidic conditions, isolated and their composition and structure determined. The ulvans contained mostly rhamnose (31.6-46.7 mol%) and glucuronic acid (26.6-37.5 mol%), with smaller amounts of xylose (3.4-10.4 mol%) and iduronic acid (3.1-7.6 mol%). In addition, the ulvan samples also contained galactose (4.4-26.0 mol%). Glycosyl linkage analysis showed that ulvan from U. ohnoi contained mostly →4)-GlcpA-(1→ and →3,4)-Rhap-(1→. Preparation of partially methylated alditol acetate standards of idose showed that U. ohnoi contained →4)-IdopA-(1→. In addition to these residues, glycosyl linkage analysis of U. tepida and U. prolifera showed the presence of →2,3,4)-Rhap-(1→, →4)-Xylp-(1→, →2,4)-GlcpA-(1→ and →3,4)-GlcpA-(1→. These two species also contained galactose linkages. These data, together with nuclear magnetic resonance (NMR) spectroscopy indicated that U. ohnoi comprised mostly of type A3S ulvanobiuronic acid repeats [→4)-ß-D-GlcpA-(1→4)-α-L-Rhap3S-(1→], together with smaller amounts of type B3S ulvanobiuronic acid repeats [→4)-α-L-IdopA-(1→4)-α-L-Rhap3S-(1→] and ulvanobiose (U3S [→4)-ß-D-Xylp-(1→4)-α-L-Rhap3S-(1→]). NMR spectra of U. tepida and U. prolifera showed resonances not detected in U. ohnoi, highlighting the complexity of the ulvans from these species. Regardless of the structural diversity of the ulvan samples there was very little antioxidant or inhibitory activity detected on enzymatic processes investigated.

Structure and rheology of pectic polysaccharides from baobab fruit and leaves.

Linkage patterns and relaxation dynamics of baobab (Adansonia digitata) polysaccharides have been investigated by means of linkage analysis and rheometry. The fruit polysaccharide was mostly xylogalacturonan, with co-extracted α-glucan. The leaf polysaccharide consists predominantly of two domains, one branched at O-4 of the →2)-Rhap-(1→ residues and another branched at O-3 of the →4)-GalpA-(1→ backbone to single GlcpA-(1→ residues. Master curves of viscoelasticity of fruit polysaccharides manifested strong pH-dependency. At pH below the dissociation constant of galacturonic acid, dispersions showed liquid-like behaviour. In contrast, at neutral pH, a weak gel network formation was observed that destabilised rapidly under the influence of flow fields. The present work identifies xylogalacturonans from baobab fruit as polysaccharides with unique rheological characteristics that may point to new directions in food and pharmaceutical formulation.

Are all ulvans equal? A comparative assessment of the chemical and gelling properties of ulvan from blade and filamentous Ulva.

Green seaweeds of the genus Ulva are rich in the bioactive sulfated polysaccharide ulvan. Herein we characterise ulvan from Ulva species collected from the Bay of Plenty, Aotearoa New Zealand. Using standardised procedures, we quantified, characterised, and compared ulvans from blade (U. australis, U. rigida, U. sp. B, and Ulva sp.) and filamentous (U. flexuosa, U. compressa, U. prolifera, and U. ralfsii) Ulva species. There were distinct differences in composition and structure of ulvans between morphologies. Ulvan isolated from blade species had higher yields (14.0-19.3 %) and iduronic acid content (IdoA = 7-18 mol%), and lower molecular weight (Mw = 190-254 kDa) and storage moduli (G' = 0.1-6.6 Pa) than filamentous species (yield = 7.2-14.6 %; IdoA = 4-7 mol%; Mw = 260-406 kDa; G' = 22.7-74.2 Pa). These results highlight the variability of the physicochemical properties of ulvan from different Ulva sources, and identifies a morphology-based division within the genus Ulva.

A protocol combining breath testing and ex vivo fermentations to study the human gut microbiome.

This protocol describes the application of breath testing and ex vivo fermentations to study the association between breath methane and the composition and functionality of the gut microbiome. The protocol provides a useful systems biology approach for studying the gut microbiome in humans, which combines standardized methods in human breath testing and fecal sampling. The model described is accessible and easy to repeat, but its relative simplicity means that it can deviate from human physiological conditions.

A novel Ka-band chirped-pulse spectrometer used in the determination of pressure broadening coefficients of astrochemical molecules.

A novel chirped-pulse Fourier transform microwave (CP-FTMW) spectrometer has been constructed to cover the Ka-band (26.5 GHz-40 GHz) for use in the CRESUCHIRP project, which aims to study the branching ratios of reactions at low temperatures using the chirped-pulse in uniform flow technique. The design takes advantage of recent developments in radio-frequency components, notably, high-frequency, high-power solid-state amplifiers. The spectrometer had a flatness of 5.5 dB across the spectral range, produced harmonic signals below -20 dBc, and the recorded signal scaled well to 6 × 106 averages. The new spectrometer was used to determine pressure broadening coefficients with a helium collider at room temperature for three molecules relevant to astrochemistry, applying the Voigt function to fit the magnitude of the Fourier-transformed data in the frequency domain. The pressure broadening coefficient for carbonyl sulfide was determined to be (2.45 ± 0.02) MHz mbar-1 at room temperature, which agreed well with previous measurements. Pressure broadening coefficients were also determined for multiple transitions of vinyl cyanide and benzonitrile. Additionally, the spectrometer was coupled with a cold, uniform flow from a Laval nozzle. The spectrum of vinyl cyanide was recorded in the flow, and its rotational temperature was determined to be (24 ± 11) K. This temperature agreed with a prediction of the composite temperature of the system through simulations of the experimental environment coupled with calculations of the solution to the optical Bloch equations. These results pave the way for future quantitative studies in low-temperature and high-pressure environments using CP-FTMW spectroscopy.

Rate Constants of the CN + Toluene Reaction from 15 to 294 K and Interstellar Implications.

CN is known for its fast reactions with hydrocarbons at low temperatures, but relatively few studies have focused on the reactions between CN and aromatic molecules. The recent detection of benzonitrile in the interstellar medium, believed to be produced by the reaction of CN and benzene, has ignited interest in studying these reactions. Here, we report rate constants of the CN + toluene (C7H8) reaction between 15 and 294 K using a CRESU (Cinétique de Réaction en Ecoulement Supersonique Uniforme; reaction kinetics in uniform supersonic flow) apparatus coupled with the pulsed laser photolysis-laser-induced fluorescence (PLP-LIF) technique. We also present the stationary points on the potential energy surface of this reaction to study the available reaction pathways. We find the rate constant does not change over this temperature range, with an average value of (4.1 ± 0.2) × 10-10 cm3 s-1, which is notably faster than the only previous measurement at 105 K. While the reason for this disagreement is unknown, we discuss the possibility that it is related to enhanced multiphoton effects in the previous work.